GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Pseudomonas putida KT2440

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate PP_0931 PP_0931 Glutamyl-tRNA(Gln) amidotransferase subunit A

Query= SwissProt::O06491
         (485 letters)



>FitnessBrowser__Putida:PP_0931
          Length = 483

 Score =  494 bits (1272), Expect = e-144
 Identities = 245/480 (51%), Positives = 335/480 (69%), Gaps = 3/480 (0%)

Query: 6   HKIT--ELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVD 63
           H++T  E+ + +  K     +L      RI+ +D ++ +F+++ E+ A   A+  D A  
Sbjct: 2   HQLTLAEIARGLADKSFSSEELTGALLARIKQLDPQINSFISVTEDLALGQARAAD-ARR 60

Query: 64  GRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLN 123
              E   L G PI  KD   T G+RT+C SK+L+NF   YDATVV +L +A  VT+GK N
Sbjct: 61  AAGETSALLGAPIAHKDLFCTNGVRTSCGSKMLDNFKAPYDATVVAKLAEAGMVTLGKTN 120

Query: 124 MDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPA 183
           MDEFAMGS+ E+S Y   KNPWNL+ VPGGSSGGSAAAVAA  +P + G+DTGGSIRQPA
Sbjct: 121 MDEFAMGSANESSHYGAVKNPWNLEHVPGGSSGGSAAAVAARLLPATTGTDTGGSIRQPA 180

Query: 184 SFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANV 243
           +   + GLKPTYGRVSR+G++A+ASSLDQ GP+ RT ED A LLQ ++G D  DSTS   
Sbjct: 181 ALTNLTGLKPTYGRVSRWGMIAYASSLDQGGPLARTAEDCALLLQGMAGFDAKDSTSIEE 240

Query: 244 DVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSK 303
            VPD+ +SL   ++GL+I +PKEY G G+     + V A++K LE LGA  +E+SLP+ +
Sbjct: 241 PVPDYSASLNASLQGLRIGLPKEYFGAGLDPRIADLVQASVKELEKLGAVVKEISLPNMQ 300

Query: 304 YALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGT 363
           +A+  YY+++ +EAS+NL+RFDG+R+GYR +   +L DLYK++R EGFG EV+RRIM+GT
Sbjct: 301 HAIPAYYVIAPAEASSNLSRFDGVRFGYRCEEPKDLTDLYKRSRGEGFGVEVQRRIMVGT 360

Query: 364 FALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYA 423
           +ALS+GYYDAYY KAQ++R LIK DF   F   D+I+GPTTP PA+K+G  + DP+  Y 
Sbjct: 361 YALSAGYYDAYYVKAQQIRRLIKNDFMAAFNDVDLILGPTTPNPAWKLGAKSSDPVAAYL 420

Query: 424 NDILTIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKP 483
            D+ TI  NLAG+PG+S+P G  DGLP+G+Q++  +F E  +  VAH ++Q TD H   P
Sbjct: 421 EDVYTITANLAGLPGLSMPAGFVDGLPVGVQLLAPYFQEGRLLNVAHRYQQVTDWHTRAP 480


Lambda     K      H
   0.315    0.134    0.381 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 558
Number of extensions: 14
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 485
Length of database: 483
Length adjustment: 34
Effective length of query: 451
Effective length of database: 449
Effective search space:   202499
Effective search space used:   202499
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate PP_0931 PP_0931 (Glutamyl-tRNA(Gln) amidotransferase subunit A)
to HMM TIGR00132 (gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit (EC 6.3.5.-))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00132.hmm
# target sequence database:        /tmp/gapView.27982.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00132  [M=466]
Accession:   TIGR00132
Description: gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.9e-180  585.5   0.0   4.4e-180  585.3   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_0931  PP_0931 Glutamyl-tRNA(Gln) amido


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0931  PP_0931 Glutamyl-tRNA(Gln) amidotransferase subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  585.3   0.0  4.4e-180  4.4e-180       5     465 ..      13     474 ..       9     475 .. 0.98

  Alignments for each domain:
  == domain 1  score: 585.3 bits;  conditional E-value: 4.4e-180
                           TIGR00132   5 lkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavkdiett 77 
                                         l +k++s++e++ ++l+ri++ + +in+f++vt++ al +a++ d++ a  e + l g pia Kd +++++++t+
  lcl|FitnessBrowser__Putida:PP_0931  13 LADKSFSSEELTGALLARIKQLDPQINSFISVTEDLALGQARAADARRAaGEtSALLGAPIAHKDLFCTNGVRTS 87 
                                         678899999************************************998876647********************* PP

                           TIGR00132  78 caSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsaaavaad 152
                                         c+Sk+L+n+++pydatVv +l eag++++GktN+DEFamGs+ e+S +g++knP+n e+vpGGSsgGsaaavaa 
  lcl|FitnessBrowser__Putida:PP_0931  88 CGSKMLDNFKAPYDATVVAKLAEAGMVTLGKTNMDEFAMGSANESSHYGAVKNPWNLEHVPGGSSGGSAAAVAAR 162
                                         *************************************************************************** PP

                           TIGR00132 153 lvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgkDkkDsts 227
                                         l p + g+DTGgSiRqPA++++  GlKPtYG+vSR+G++ayasSldq G+la++ ed al+l+ ++g D+kDsts
  lcl|FitnessBrowser__Putida:PP_0931 163 LLPATTGTDTGGSIRQPAALTNLTGLKPTYGRVSRWGMIAYASSLDQGGPLARTAEDCALLLQGMAGFDAKDSTS 237
                                         *************************************************************************** PP

                           TIGR00132 228 levkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvklalaiYyiisps 302
                                         +e +v+++  +l++ l+gl++g+ ke+++ +ld ++++ +++ +++le+lga ++e+slp+++ a+++Yy+i+p+
  lcl|FitnessBrowser__Putida:PP_0931 238 IEEPVPDYSASLNASLQGLRIGLPKEYFGAGLDPRIADLVQASVKELEKLGAVVKEISLPNMQHAIPAYYVIAPA 312
                                         *************************************************************************** PP

                           TIGR00132 303 EassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykkAqkvrtliidefe 377
                                         Eassnl+r+dg+r+G+r ee+k+l++ly+++R egfg ev+rRim+G+yals++yyd+yy kAq++r+li+++f 
  lcl|FitnessBrowser__Putida:PP_0931 313 EASSNLSRFDGVRFGYRCEEPKDLTDLYKRSRGEGFGVEVQRRIMVGTYALSAGYYDAYYVKAQQIRRLIKNDFM 387
                                         *************************************************************************** PP

                           TIGR00132 378 klfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkk 452
                                          +f++vD+i++pt+p  a klg+k +dp++ yl+Dv+t++anlaGlp++s+P+g   +glp+G+q+ + +f++ +
  lcl|FitnessBrowser__Putida:PP_0931 388 AAFNDVDLILGPTTPNPAWKLGAKSSDPVAAYLEDVYTITANLAGLPGLSMPAGFV-DGLPVGVQLLAPYFQEGR 461
                                         ********************************************************.7***************** PP

                           TIGR00132 453 llsvakaleqald 465
                                         ll+va+ ++q +d
  lcl|FitnessBrowser__Putida:PP_0931 462 LLNVAHRYQQVTD 474
                                         ********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (483 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.40
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory